bio 1.2.1 → 1.3.0

data/lib/bio/db/embl/sptr.rb

@@ -4,7 +4,7 @@
 # Copyright::   Copyright (C) 2001-2006  Mitsuteru C. Nakao <n@bioruby.org>
 # License::     The Ruby License
 #
-# $Id: sptr.rb,v 1.36 2007/04/05 23:35:40 trevor Exp $
+# $Id:$
 #
 # == Description
 # 
@@ -241,7 +241,7 @@ class SPTR < EMBLDB
     records = gn_line.split(/\s*and\s*/)
     records.each do |record|
       gene_hash = {:name => '', :synonyms => [], :loci => [], :orfs => []}
-      record.each(';') do |element|
+      record.each_line(';') do |element|
         case element
         when /Name=/ then
           gene_hash[:name] = $'[0..-2]
@@ -505,11 +505,10 @@ class SPTR < EMBLDB
             else
               hash['journal'] = value
             end
-          when 'RX'  # PUBMED, MEDLINE
-            value.split('.').each {|item|
-              tag, xref = item.split(/; /).map {|i| i.strip }
+          when 'RX'  # PUBMED, MEDLINE, DOI
+            value.each do |tag, xref|
               hash[ tag.downcase ]  = xref
-            }
+            end
           end
         }
         Reference.new(hash)
@@ -678,17 +677,17 @@ class SPTR < EMBLDB
     when 'COFACTOR'
       return @data['CC'][topic]
     when 'DEVELOPMENTAL STAGE'
-      return @data['CC'][topic].to_s
+      return @data['CC'][topic].join('')
     when 'DISEASE'
-      return @data['CC'][topic].to_s
+      return @data['CC'][topic].join('')
     when 'DOMAIN'
       return @data['CC'][topic]
     when 'ENZYME REGULATION'
-      return @data['CC'][topic].to_s
+      return @data['CC'][topic].join('')
     when 'FUNCTION'
-      return @data['CC'][topic].to_s
+      return @data['CC'][topic].join('')
     when 'INDUCTION'
-      return @data['CC'][topic].to_s
+      return @data['CC'][topic].join('')
     when 'INTERACTION'
       return cc_interaction(@data['CC'][topic])
     when 'MASS SPECTROMETRY'
@@ -749,7 +748,7 @@ class SPTR < EMBLDB
 
 
   def cc_alternative_products(data)
-    ap = data.to_s
+    ap = data.join('')
     return ap unless ap
 
     # Event, Named isoforms, Comment, [Name, Synonyms, IsoId, Sequnce]+
@@ -822,7 +821,7 @@ class SPTR < EMBLDB
 
 
   def cc_caution(data)
-    data.to_s
+    data.join('')
   end
   private :cc_caution
 
@@ -831,7 +830,7 @@ class SPTR < EMBLDB
   #
   #   CC       P46527:CDKN1B; NbExp=1; IntAct=EBI-359815, EBI-519280;
   def cc_interaction(data)
-    str = data.to_s
+    str = data.join('')
     it = str.scan(/(.+?); NbExp=(.+?); IntAct=(.+?);/)
     it.map {|ent|
       ent.map! {|x| x.strip }
@@ -894,7 +893,7 @@ class SPTR < EMBLDB
 
 
   def cc_rna_editing(data)
- data = data.to_s
+    data = data.join('')
     entry = {'Modified_positions' => [], 'Note' => ""}
     if data =~ /Modified_positions=(.+?)(\.|;)/
       entry['Modified_positions'] = $1.sub(/\.$/, '').split(', ')
@@ -961,7 +960,7 @@ class SPTR < EMBLDB
     unless key
       embl_dr
     else
-      embl_dr[key].map {|x|
+      (embl_dr[key] or []).map {|x|
         {'Accession' => x[0],
          'Version' => x[1],
          ' ' => x[2],

data/lib/bio/db/fantom.rb

@@ -4,13 +4,11 @@
 # Copyright:: Copyright (C) 2003 GOTO Naohisa <ng@bioruby.org> 
 # License::   The Ruby License
 #
-#  $Id: fantom.rb,v 1.14 2007/04/05 23:35:40 trevor Exp $
+#  $Id:$
 #
 
-begin
-  require 'rexml/document'
-  rescue LoadError
-end
+require 'rexml/document'
+require 'cgi'
 require 'uri'
 require 'net/http'
 
@@ -32,17 +30,17 @@ module Bio
     def get_by_id(idstr, http_proxy = nil)
       addr = 'fantom.gsc.riken.go.jp'
       port = 80
-      path = "/db/maxml/maxmlseq.cgi?masterid=#{URI.escape(idstr.to_s)}&style=xml"
+      path = "/db/maxml/maxmlseq.cgi?masterid=#{CGI.escape(idstr.to_s)}&style=xml"
       xml = ''
       if http_proxy then
         proxy = URI.parse(http_proxy.to_s)
         Net::HTTP.start(addr, port, proxy.host, proxy.port) do |http|
-          response, = http.get(path)
+          response = http.get(path)
           xml = response.body
         end
       else
         Bio::Command.start_http(addr, port) do |http|
-          response, = http.get(path)
+          response = http.get(path)
           xml = response.body
         end
       end

data/lib/bio/db/fasta.rb

@@ -2,11 +2,11 @@
 # = bio/db/fasta.rb - FASTA format class
 #
 # Copyright::  Copyright (C) 2001, 2002
-#              GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>,
+#              Naohisa Goto <ng@bioruby.org>,
 #              Toshiaki Katayama <k@bioruby.org>
 # License::    The Ruby License
 #
-# $Id: fasta.rb,v 1.28 2007/04/05 23:35:40 trevor Exp $
+# $Id: fasta.rb,v 1.28.2.3 2008/06/20 13:43:36 ngoto Exp $
 # 
 # == Description
 # 
@@ -14,45 +14,7 @@
 #
 # == Examples
 #
-#       rub = Bio::FastaDefline.new('>gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]')
-#       rub.entry_id       ==> 'gi|671595'
-#       rub.get('emb')     ==> 'CAA85678.1'
-#       rub.emb            ==> 'CAA85678.1'
-#       rub.gi             ==> '671595'
-#       rub.accession      ==> 'CAA85678'
-#       rub.accessions     ==> [ 'CAA85678' ]
-#       rub.acc_version    ==> 'CAA85678.1'
-#       rub.locus          ==> nil
-#       rub.list_ids       ==> [["gi", "671595"],
-#                               ["emb", "CAA85678.1", nil],
-#                               ["Perovskia abrotanoides"]]
-#
-#       ckr = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]")
-#       ckr.entry_id      ==> "gi|2495000"
-#       ckr.sp            ==> "CCKR_CAVPO"
-#       ckr.pir           ==> "I51898"
-#       ckr.gb            ==> "AAB29504.1"
-#       ckr.gi            ==> "2495000"
-#       ckr.accession     ==> "AAB29504"
-#       ckr.accessions    ==> ["Q63931", "AAB29504"]
-#       ckr.acc_version   ==> "AAB29504.1"
-#       ckr.locus         ==> nil
-#       ckr.description   ==>
-#         "CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)"
-#       ckr.descriptions  ==>
-#         ["CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)",
-#          "cholecystokinin A receptor - guinea pig",
-#          "cholecystokinin A receptor; CCK-A receptor [Cavia]"]
-#       ckr.words         ==> 
-#         ["cavia", "cck-a", "cck-ar", "cholecystokinin", "guinea", "pig",
-#          "receptor", "type"]
-#       ckr.id_strings    ==>
-#         ["2495000", "Q63931", "CCKR_CAVPO", "2147182", "I51898",
-#          "544724", "AAB29504.1", "Cavia"]
-#       ckr.list_ids      ==>
-#         [["gi", "2495000"], ["sp", "Q63931", "CCKR_CAVPO"],
-#          ["gi", "2147182"], ["pir", nil, "I51898"], ["gi", "544724"],
-#          ["gb", "AAB29504.1", nil], ["Cavia"]]
+# See documents of Bio::FastaFormat class.
 #
 # == References
 #
@@ -65,6 +27,8 @@
 
 require 'bio/db'
 require 'bio/sequence'
+require 'bio/sequence/dblink'
+require 'bio/db/fasta/defline'
 
 module Bio
 
@@ -81,7 +45,7 @@ module Bio
   #
   # === Examples
   #
-  #   f_str = <<END
+  #   f_str = <<END_OF_STRING
   #   >sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
   #   MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG
   #   VPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME
@@ -101,7 +65,7 @@ module Bio
   #   CNELVKRHLQFNPNKLTKFYTLQPMDVLLPILEKALNLSQIRVKPDLFAN
   #   FERLCELLGYDNVFPLIINIKTKSNGGYQLCGSISIIKIEEELKSVGFER
   #   KTGDPLEWRRLFKKISTICRDIILIPN
-  #   END
+  #   END_OF_STRING
   #
   #   f = Bio::FastaFormat.new(f_str)
   #   puts "### FastaFormat"
@@ -253,12 +217,10 @@ module Bio
     # might also be changed (but not always be changed)
     # because of efficiency.
     # 
-    def to_seq
-      seq
-      obj = Bio::Sequence.new(@seq)
-      obj.definition = self.definition
-      obj
+    def to_biosequence
+      Bio::Sequence.adapter(self, Bio::Sequence::Adapter::FastaFormat)
     end
+    alias to_seq to_biosequence
 
     # Parsing FASTA Defline, and extract IDs.
     # IDs are NSIDs (NCBI standard FASTA sequence identifiers)
@@ -362,465 +324,6 @@ module Bio
 
   end #class FastaNumericFormat
 
-
-  # Parsing FASTA Defline, and extract IDs and other informations.
-  # IDs are NSIDs (NCBI standard FASTA sequence identifiers)
-  # or ":"-separated IDs.
-  # 
-  # specs are described in:
-  # ftp://ftp.ncbi.nih.gov/blast/documents/README.formatdb
-  # http://blast.wustl.edu/doc/FAQ-Indexing.html#Identifiers
-  #
-  # === Examples
-  #
-  #   rub = Bio::FastaDefline.new('>gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]')
-  #   rub.entry_id       ==> 'gi|671595'
-  #   rub.get('emb')     ==> 'CAA85678.1'
-  #   rub.emb            ==> 'CAA85678.1'
-  #   rub.gi             ==> '671595'
-  #   rub.accession      ==> 'CAA85678'
-  #   rub.accessions     ==> [ 'CAA85678' ]
-  #   rub.acc_version    ==> 'CAA85678.1'
-  #   rub.locus          ==> nil
-  #   rub.list_ids       ==> [["gi", "671595"],
-  #                           ["emb", "CAA85678.1", nil],
-  #                           ["Perovskia abrotanoides"]]
-  #
-  #   ckr = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]")
-  #   ckr.entry_id      ==> "gi|2495000"
-  #   ckr.sp            ==> "CCKR_CAVPO"
-  #   ckr.pir           ==> "I51898"
-  #   ckr.gb            ==> "AAB29504.1"
-  #   ckr.gi            ==> "2495000"
-  #   ckr.accession     ==> "AAB29504"
-  #   ckr.accessions    ==> ["Q63931", "AAB29504"]
-  #   ckr.acc_version   ==> "AAB29504.1"
-  #   ckr.locus         ==> nil
-  #   ckr.description   ==>
-  #     "CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)"
-  #   ckr.descriptions  ==>
-  #     ["CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)",
-  #      "cholecystokinin A receptor - guinea pig",
-  #      "cholecystokinin A receptor; CCK-A receptor [Cavia]"]
-  #   ckr.words         ==> 
-  #     ["cavia", "cck-a", "cck-ar", "cholecystokinin", "guinea", "pig",
-  #      "receptor", "type"]
-  #   ckr.id_strings    ==>
-  #     ["2495000", "Q63931", "CCKR_CAVPO", "2147182", "I51898",
-  #      "544724", "AAB29504.1", "Cavia"]
-  #   ckr.list_ids      ==>
-  #     [["gi", "2495000"], ["sp", "Q63931", "CCKR_CAVPO"],
-  #      ["gi", "2147182"], ["pir", nil, "I51898"], ["gi", "544724"],
-  #      ["gb", "AAB29504.1", nil], ["Cavia"]]
-  #
-  # === Refereneces
-  #
-  # * Fasta format description (NCBI)
-  #   http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
-  #
-  # * Frequently Asked Questions:  Indexing of Sequence Identifiers (by Warren R. Gish.)
-  #   http://blast.wustl.edu/doc/FAQ-Indexing.html#Identifiers
-  #
-  # * README.formatdb
-  #   ftp://ftp.ncbi.nih.gov/blast/documents/README.formatdb
-  # 
-  class FastaDefline
-
-    NSIDs = {
-      # NCBI and WU-BLAST
-      'gi'  => [ 'gi' ],                      # NCBI GI
-      'gb'  => [ 'acc_version', 'locus' ],      # GenBank
-      'emb' => [ 'acc_version', 'locus' ],      # EMBL
-      'dbj' => [ 'acc_version', 'locus' ],      # DDBJ
-      'sp'  => [ 'accession', 'entry_id' ],   # SWISS-PROT
-      'pdb' => [ 'entry_id', 'chain' ],       # PDB
-      'bbs' => [ 'number' ],                  # GenInfo Backbone Id
-      'gnl' => [ 'database' , 'entry_id' ],   # General database identifier
-      'ref' => [ 'acc_version' , 'locus' ],     # NCBI Reference Sequence
-      'lcl' => [ 'entry_id' ],                # Local Sequence identifier
-
-      # WU-BLAST and NCBI
-      'pir' => [ 'accession', 'entry_id' ],   # PIR
-      'prf' => [ 'accession', 'entry_id' ],   # Protein Research Foundation
-      'pat' => [ 'country', 'number', 'serial' ], # Patents
-
-      # WU-BLAST only
-      'bbm' => [ 'number' ],      # NCBI GenInfo Backbone database identifier
-      'gim' => [ 'number' ],      # NCBI GenInfo Import identifier
-      'gp'  => [ 'acc_version', 'locus' ],      # GenPept
-      'oth' => [ 'accession', 'name', 'release' ],  # Other (user-definable) identifier
-      'tpd' => [ 'accession', 'name' ],       # Third party annotation, DDBJ
-      'tpe' => [ 'accession', 'name' ],       # Third party annotation, EMBL
-      'tpg' => [ 'accession', 'name' ],       # Third party annotation, GenBank
-
-      # Original
-      'ri'  => [ 'entry_id', 'rearray_id', 'len' ], # RIKEN FANTOM DB
-    }
-
-    # Shows array that contains IDs (or ID-like strings).
-    # Returns an array of arrays of strings.
-    attr_reader :list_ids
-
-    # Shows a possibly unique identifier.
-    # Returns a string.
-    attr_reader :entry_id
-
-    # Parses given string.
-    def initialize(str)
-      @deflines = []
-      @info = {}
-      @list_ids = []
-
-      @entry_id = nil
-
-      lines = str.split("\x01")
-      lines.each do |line|
-        add_defline(line)
-      end
-    end #def initialize
-
-    # Parses given string and adds parsed data.
-    def add_defline(str)
-      case str
-      when /^\>?\s*((?:[^\|\s]*\|)+[^\s]+)\s*(.*)$/
-        # NSIDs
-        # examples:
-        # >gi|9910844|sp|Q9UWG2|RL3_METVA 50S ribosomal protein L3P
-        #
-        # note: regexp (:?) means grouping without backreferences
-        i = $1
-        d = $2
-        tks = i.split('|')
-        tks << '' if i[-1,1] == '|'
-        a = parse_NSIDs(tks)
-        i = a[0].join('|')
-        a.unshift('|')
-        d = tks.join('|') + ' ' + d unless tks.empty?
-        a << d
-        this_line = a
-        match_EC(d)
-        parse_square_brackets(d).each do |x|
-          if !match_EC(x, false) and x =~ /\A[A-Z]/ then
-            di = [  x ]
-            @list_ids << di
-            @info['organism'] = x unless @info['organism']
-          end
-        end
-
-      when /^\>?\s*([a-zA-Z0-9]+\:[^\s]+)\s*(.*)$/
-        # examples:
-        # >sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
-        # >emb:CACDC28 [X80034] C.albicans CDC28 gene 
-        i = $1
-        d = $2
-        a = parse_ColonSepID(i)
-        i = a.join(':')
-        this_line = [ ':', a , d ]
-        match_EC(d)
-        parse_square_brackets(d).each do |x|
-          if !match_EC(x, false) and x =~ /:/ then
-            parse_ColonSepID(x)
-          elsif x =~ /\A\s*([A-Z][A-Z0-9_\.]+)\s*\z/ then
-            @list_ids << [ $1 ]
-          end
-        end
-
-      when /^\>?\s*(\S+)(?:\s+(.+))?$/
-        # examples:
-        # >ABC12345 this is test
-        i = $1
-        d = $2.to_s
-        @list_ids << [ i.chomp('.') ]
-        this_line = [  '', [ i ], d ]
-        match_EC(d)
-      else
-        i = str
-        d = ''
-        match_EC(i)
-        this_line = [ '', [ i ], d ]
-      end
-
-      @deflines << this_line
-      @entry_id = i unless @entry_id
-    end
-
-    def match_EC(str, write_flag = true)
-      di = nil
-      str.scan(/EC\:((:?[\-\d]+\.){3}(:?[\-\d]+))/i) do |x|
-        di = [ 'EC', $1 ]
-        if write_flag then
-          @info['ec'] = di[1] if (!@info['ec'] or @info['ec'].to_s =~ /\-/)
-          @list_ids << di
-        end
-      end
-      di
-    end
-    private :match_EC
-
-    def parse_square_brackets(str)
-      r = []
-      str.scan(/\[([^\]]*)\]/) do |x|
-        r << x[0]
-      end
-      r
-    end
-    private :parse_square_brackets
-
-    def parse_ColonSepID(str)
-      di = str.split(':', 2)
-      di << nil if di.size <= 1 
-      @list_ids << di
-      di
-    end
-    private :parse_ColonSepID
-
-    def parse_NSIDs(ary)
-      # this method destroys ary
-      data = []
-      while token = ary.shift
-        if labels = self.class::NSIDs[token] then
-          di = [ token ]
-          idtype = token
-          labels.each do |x|
-            token = ary.shift
-            break unless token
-            if self.class::NSIDs[token] then
-              ary.unshift(token)
-              break #each
-            end
-            if token.length > 0 then
-              di << token
-            else
-              di << nil
-            end
-          end
-          data << di
-        else
-          if token.length > 0 then
-            # UCID (uncontrolled identifiers)
-            di = [ token ]
-            data << di
-            @info['ucid'] = token unless @info['ucid']
-          end
-          break #while
-        end
-      end #while
-      @list_ids.concat data
-      data
-    end #def parse_NSIDs
-    private :parse_NSIDs
-
-
-    # Shows original string.
-    # Note that the result of this method may be different from
-    # original string which is given in FastaDefline.new method.
-    def to_s
-      @deflines.collect { |a|
-        s = a[0]
-        (a[1..-2].collect { |x| x.join(s) }.join(s) + ' ' + a[-1]).strip
-      }.join("\x01")
-    end
-
-    # Shows description.
-    def description
-      @deflines[0].to_a[-1]
-    end
-
-    # Returns descriptions.
-    def descriptions
-      @deflines.collect do |a|
-        a[-1]
-      end
-    end
-
-    # Shows ID-like strings.
-    # Returns an array of strings.
-    def id_strings
-      r = []
-      @list_ids.each do |a|
-        if a.size >= 2 then
-          r.concat a[1..-1].find_all { |x| x }
-        else
-          if a[0].to_s.size > 0 and a[0] =~ /\A[A-Za-z0-9\.\-\_]+\z/
-            r << a[0]
-          end
-        end
-      end
-      r.concat( words(true, []).find_all do |x|
-                 x =~ /\A[A-Z][A-Za-z0-9\_]*[0-9]+[A-Za-z0-9\_]+\z/ or
-                   x =~ /\A[A-Z][A-Z0-9]*\_[A-Z0-9\_]+\z/
-               end)
-      r
-    end
-
-    KillWords = [
-      'an', 'the', 'this', 'that',
-      'is', 'are', 'were', 'was', 'be', 'can', 'may', 'might',
-      'as', 'at', 'by', 'for', 'in', 'of', 'on', 'to', 'with',
-      'from', 'and', 'or', 'not',
-      'dna', 'rna', 'mrna', 'cdna', 'orf',
-      'aa', 'nt', 'pct', 'id', 'ec', 'sp', 'subsp',
-      'similar', 'involved', 'identical', 'identity',
-      'cds', 'clone', 'library', 'contig', 'contigs',
-      'homolog', 'homologue', 'homologs', 'homologous',
-      'protein', 'proteins', 'gene', 'genes',
-      'product', 'products', 'sequence', 'sequences', 
-      'strain', 'strains', 'region', 'regions',
-    ]
-    KillWordsHash = {}
-    KillWords.each { |x| KillWordsHash[x] = true }
-
-    KillRegexpArray = [
-      /\A\d{1,3}\%?\z/,
-      /\A[A-Z][A-Za-z0-9\_]*[0-9]+[A-Za-z0-9\_]+\z/,
-      /\A[A-Z][A-Z0-9]*\_[A-Z0-9\_]+\z/
-    ]
-
-    # Shows words used in the defline. Returns an Array.
-    def words(case_sensitive = nil, kill_regexp = self.class::KillRegexpArray,
-              kwhash = self.class::KillWordsHash)
-      a = descriptions.join(' ').split(/[\.\,\;\:\(\)\[\]\{\}\<\>\"\'\`\~\/\|\?\!\&\@\#\s\x00-\x1f\x7f]+/)
-      a.collect! do |x|
-        x.sub!(/\A[\$\*\-\+]+/, '')
-        x.sub!(/[\$\*\-\=]+\z/, '')
-        if x.size <= 1 then
-          nil
-        elsif kwhash[x.downcase] then
-          nil
-        else
-          if kill_regexp.find { |expr| expr =~ x } then
-            nil
-          else
-            x
-          end
-        end
-      end
-      a.compact!
-      a.collect! { |x| x.downcase } unless case_sensitive
-      a.sort!
-      a.uniq!
-      a
-    end
-
-    # Returns identifires by a database name.
-    def get(dbname)
-      db = dbname.to_s
-      r = nil
-      unless r = @info[db] then
-        di = @list_ids.find { |x| x[0] == db.to_s }
-        if di and di.size <= 2 then
-          r = di[-1]
-        elsif di then
-          labels = self.class::NSIDs[db]
-          [ 'acc_version', 'entry_id',
-            'locus', 'accession', 'number'].each do |x|
-            if i = labels.index(x) then
-              r = di[i+1]
-              break if r
-            end
-          end
-          r = di[1..-1].find { |x| x } unless r
-        end
-        @info[db] = r if r
-      end
-      r
-    end
-
-    # Returns an identifier by given type.
-    def get_by_type(type_str)
-      @list_ids.each do |x|
-        if labels = self.class::NSIDs[x[0]] then
-          if i = labels.index(type_str) then
-            return x[i+1]
-          end
-        end
-      end
-      nil
-    end
-
-    # Returns identifiers by given type.
-    def get_all_by_type(*type_strarg)
-      d = []
-      @list_ids.each do |x|
-        if labels = self.class::NSIDs[x[0]] then
-          type_strarg.each do |y|
-            if i = labels.index(y) then
-              d << x[i+1] if x[i+1]
-            end
-          end
-        end
-      end
-      d
-    end
-
-    # Shows locus.
-    # If the entry has more than two of such IDs,
-    # only the first ID are shown.
-    # Returns a string or nil.
-    def locus
-      unless defined?(@locus)
-        @locus = get_by_type('locus')
-      end
-      @locus
-    end
-
-    # Shows GI.
-    # If the entry has more than two of such IDs,
-    # only the first ID are shown.
-    # Returns a string or nil.
-    def gi
-      unless defined?(@gi) then
-        @gi = get_by_type('gi')
-      end
-      @gi
-    end
-
-    # Shows accession with version number.
-    # If the entry has more than two of such IDs,
-    # only the first ID are shown.
-    # Returns a string or nil.
-    def acc_version
-      unless defined?(@acc_version) then
-        @acc_version = get_by_type('acc_version')
-      end
-      @acc_version
-    end
-
-    # Shows accession numbers.
-    # Returns an array of strings.
-    def accessions
-      unless defined?(@accessions) then
-        @accessions = get_all_by_type('accession', 'acc_version')
-        @accessions.collect! { |x| x.sub(/\..*\z/, '') }
-      end
-      @accessions
-    end
-
-    # Shows an accession number.
-    def accession
-      unless defined?(@accession) then
-        if acc_version then
-          @accession = acc_version.split('.')[0]
-        else
-          @accession = accessions[0]
-        end
-      end
-      @accession
-    end
-    
-    def method_missing(name, *args)
-      # raise ArgumentError,
-      # "wrong # of arguments(#{args.size} for 1)" if args.size >= 2
-      r = get(name, *args)
-      if !r and !(self.class::NSIDs[name.to_s]) then
-        raise "NameError: undefined method `#{name.inspect}'"
-      end
-      r
-    end
-    
-
-  end #class FastaDefline
-
 end #module Bio
 
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